1.Print quality table as requested in scenario:

Case rates by month for different regions within the EU.

summary_table1<- joined_df%>%
  group_by(sub_region, month_rep)%>%
  summarise(total_case_region= sum(total_conf_case))%>%
  mutate(monthly_cases_per_region= sum(total_case_region), 
  MPX_cases_rate_per_region =
    round( total_case_region/monthly_cases_per_region*100,1))%>%
  arrange(sub_region, desc(month_rep))
## `summarise()` has grouped output by 'sub_region'. You can override using the
## `.groups` argument.
kable(summary_table1, 
      booktabs=T, 
      col.names=c("EU Regions", "Months  MPX cases reported", "MPX cases", 
                  "Total MPX cases per region", 
                  "MPX cases rate per month per region"),  
      align='lcccc', 
caption="MonkeyPox Rates per month for different regions within the EU in 2022",
      format.args=list(big.mark=","))
MonkeyPox Rates per month for different regions within the EU in 2022
EU Regions Months MPX cases reported MPX cases Total MPX cases per region MPX cases rate per month per region
Eastern Europe May 5 277 1.8
Eastern Europe June 58 277 20.9
Eastern Europe July 116 277 41.9
Eastern Europe August 98 277 35.4
Northern Europe May 16 576 2.8
Northern Europe June 117 576 20.3
Northern Europe July 246 576 42.7
Northern Europe August 197 576 34.2
Southern Europe May 422 7,906 5.3
Southern Europe June 1,902 7,906 24.1
Southern Europe July 3,773 7,906 47.7
Southern Europe August 1,809 7,906 22.9
Western Europe May 131 8,257 1.6
Western Europe June 2,040 8,257 24.7
Western Europe July 4,134 8,257 50.1
Western Europe August 1,952 8,257 23.6

1.1 Print quality plot or chart as requested in scenario

summary_table1$month_rep<- factor(summary_table1$month_rep)                     
    
    summary_table1 %>% 
      ggplot(aes( x=sub_region, y= MPX_cases_rate_per_region,fill=month_rep)) +
      geom_bar(position="dodge",stat="identity")+
      labs(x = "EU Regions", y = "MonkeyPox Cases Rate")+
      ggtitle("Dodged bar chart of monkeypox case rates by 
      month for different regions within the EU")

Interpretation:

1.2 Print quality plot or chart as requested in scenario

#make a presentable table
plot_ly(
  summary_table1,
  x=~ month_rep,
  y=~MPX_cases_rate_per_region,
  color=~sub_region,
  type="scatter",
  mode="lines",
  colors=c("darkorange","darkcyan","darkslateblue", "darkred")
  #text = ~paste('Cases: ',cases,'<br>Population: ',population,'<br>Rate: ',rate)
) %>%
  layout(
    title="Alameda County STD Rates, 2001-2018",
    yaxis=list(title="Case Rate per 100,000"),
    xaxis=list(title="Year"),
    paper_bgcolor="azure",
    plot_bgcolor="white"
  )
## Warning: `arrange_()` was deprecated in dplyr 0.7.0.
## Please use `arrange()` instead.
## See vignette('programming') for more help
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
 female_summary<- total_dataset%>%
  mutate(mpx_rate = round(total_mpx_case/ sum(sex_female) *100,2))%>%
  select(country_code, total_mpx_case, sex_female, mpx_rate)%>%
  rename(female_population = sex_female)
female_summary
scatter_plot <- ggplot(data = female_summary, aes(x = female_population,
                                                 y = mpx_rate)) + 
  geom_point(na.rm=TRUE) + theme_minimal(base_size = 15)+
  labs(x = " Total Number of females", 
       y = "Total number of MonkeyPox cases",
     title ="Relationship between MonkeyPox cases and
     Numbers of females within EU")
scatter_plot

Interpretation:

male_summary<- total_dataset%>%
  mutate(mpx_rate = round(total_mpx_case/ sum(sex_male) *100,2))%>%
  select(country_code, total_mpx_case, sex_male, mpx_rate)%>%
  rename(male_population = sex_male)
female_summary
scatter_plot <- ggplot(data = male_summary, aes(x = male_population,
                                                 y = mpx_rate)) + 
  geom_point(na.rm=TRUE) + theme_minimal(base_size = 15)+
  labs(x = " Total Number of males", 
       y = "Total number of MonkeyPox cases",
     title ="Relationship between MonkeyPox cases and
     Numbers of males within EU")
scatter_plot